Results (PhD Chapter 2)
Section 1/2
This series of files compile all analyses done during Chapter 2:
- Section 1 regroups maps.
- Section 2 presents regressions and HMSC results.
All analyses have been done with R 3.6.0.
Click on the table of contents in the left margin to assess a specific analysis
Click on a figure to zoom it
To assess Section 2, click here.
To go back to the summary page, click here.
Human activities considered for the analyses:
- city influence: CityInf
- industries influence: InduInf
- dredging dumping sites: DredSit
- commercial ships mooring site: MoorSit
- rainwater sewers: RainSew
- wastewater sewers: WastSew
- city wharves: CityWha
- industries wharves: InduWha
- fisheries (gear used):
- traps: FishTrap
- bottom-trawling: FishTraw
- longline: FishLine
- nets: FishNet
- dredge: FishDred
Data is also available for the number of captured individuals for dogwhelk (Buccinum sp.), common crab (Cancer irroratus), snowcrab (Chinoecetes opilio), nordic shrimp (Pandalus borealis), arctic surfclam (Mactromeris polynyma) and american lobster (Homarus americanus) fisheries.
Workspace preparation
library(marmap)
library(pander)
library(raster)
library(reshape2)
library(sf)
library(stats)
library(tidyverse)Here, we use data from subtidal ecosystems (see metadata files for more information)
Only stations that have been sampled both for abiotic parameters and benthic species were included.
The script below includes personnal functions, refined data, parameters for each campaign and global means, sd, se.
1. Maps
Depth
Isobaths
2. Modelling of human activities influence (WIP)
The influence of each human activity has been modelled at each station, in order to be later used in HMSC models.
We calculated a probability of influence for each activity \(P_{ij}\). For non-fisheries activities, the index \(I_{ij}\) has been calculated based on the distance from the source(s), bathymetry and hydrodynamics influences. We also included a weighting parameter specific for each activity, .
\[ P_{ij} = w_{j} . I_{ij} \]
\[ I_{ij} = \left( 1 - \frac{D_{ij}}{D_{max, j}} \right) . f_{j} \left( 1 - \frac{D_{ij}}{D_{max, j}} \right) . \Delta Z_{i} . H_{i} \]
- \(i\) is a station
- \(j\) is a human activity
- \(f_{j}\) is the decay function of activity \(j\)
- \(w_{j}\) is the weighting parameter for activity \(j\)
- \(D_{ij}\) is the distance of station \(i\) from the source of activity \(j\)
- \(\Delta Z_{i}\) is the bathymetry index at station \(i\)
- \(H_{i}\) is the hydrodynamic index at station \(i\)
i) Distance form the source
This corresponds to \(D_{ij}\) in Formula 2.
First, we need to calculate the distance of each station from the source(s) of the activity. This proxy will allow to take coasts and island into consideration (necessary at BSI), and will then be used to calculated the probabilities of influence.
Here are the minimum distances of each station from the source of each activity (in meters, calculated with gdistance):
| station_id | city | dredging | industry | mooring | sewers_rain | sewers_waste | wharves_city | wharves_industry |
|---|---|---|---|---|---|---|---|---|
| 1 | 8090 | 1141 | 361 | 1012 | 2099 | 1321 | 8334 | 275 |
| 2 | 7364 | 742 | 186 | 1445 | 1085 | 186 | 7339 | 165 |
| 3 | 8053 | 1085 | 171 | 1156 | 1910 | 1131 | 8240 | 86 |
| 4 | 8246 | 1354 | 542 | 949 | 2356 | 1578 | 8548 | 532 |
| 5 | 8215 | 1415 | 763 | 742 | 2565 | 1786 | 8622 | 741 |
| 6 | 6273 | 1568 | 330 | 2282 | 491 | 1473 | 6202 | 428 |
| 7 | 6154 | 1592 | 433 | 2267 | 609 | 1540 | 6083 | 546 |
| 8 | 6961 | 1177 | 495 | 2044 | 516 | 722 | 6890 | 119 |
| 9 | 6984 | 1073 | 447 | 1941 | 577 | 618 | 6913 | 238 |
| 10 | 7809 | 949 | 0 | 1383 | 1377 | 599 | 7861 | 119 |
| 11 | 542 | 4253 | 2138 | 1880 | 3744 | 4211 | 618 | 2899 |
| 12 | 424 | 4111 | 1996 | 1984 | 3832 | 4299 | 447 | 2757 |
| 13 | 594 | 4324 | 2209 | 1828 | 3723 | 4190 | 703 | 2970 |
| 14 | 661 | 4276 | 2162 | 1761 | 3805 | 4272 | 684 | 2922 |
| 15 | 532 | 4015 | 1900 | 1850 | 3966 | 4433 | 447 | 2661 |
| 16 | 1850 | 447 | 165 | 4247 | 5300 | 7968 | 1850 | 665 |
| 17 | 1627 | 722 | 82 | 3972 | 5105 | 7745 | 1627 | 424 |
| 18 | 1523 | 893 | 186 | 3800 | 4963 | 7642 | 1523 | 351 |
| 19 | NA | NA | NA | NA | NA | NA | NA | NA |
| 20 | 0 | 2253 | 119 | 2813 | 5007 | 6118 | 0 | 899 |
| 21 | NA | NA | NA | NA | NA | NA | NA | NA |
| 22 | NA | NA | NA | NA | NA | NA | NA | NA |
| 23 | NA | NA | NA | NA | NA | NA | NA | NA |
| 24 | NA | NA | NA | NA | NA | NA | NA | NA |
| 25 | NA | NA | NA | NA | NA | NA | NA | NA |
| 26 | 11612 | 10102 | 10643 | 11620 | 8952 | 12003 | 11612 | 10851 |
| 27 | 11746 | 10236 | 10777 | 11754 | 9086 | 12137 | 11746 | 10985 |
| 28 | NA | NA | NA | NA | NA | NA | NA | NA |
| 29 | NA | NA | NA | NA | NA | NA | NA | NA |
| 30 | 11509 | 9998 | 10539 | 11517 | 8848 | 11899 | 11509 | 10747 |
| 31 | 7883 | 4608 | 5808 | 9963 | 10412 | 13492 | 7883 | 6699 |
| 32 | 7883 | 4608 | 5808 | 9963 | 10412 | 13492 | 7883 | 6699 |
| 33 | NA | NA | NA | NA | NA | NA | NA | NA |
| 34 | 7764 | 4490 | 5689 | 9858 | 10346 | 13425 | 7764 | 6580 |
| 35 | 7741 | 4466 | 5685 | 9821 | 10241 | 13321 | 7741 | 6557 |
| 36 | NA | NA | NA | NA | NA | NA | NA | NA |
| 37 | NA | NA | NA | NA | NA | NA | NA | NA |
| 38 | NA | NA | NA | NA | NA | NA | NA | NA |
| 39 | NA | NA | NA | NA | NA | NA | NA | NA |
| 40 | NA | NA | NA | NA | NA | NA | NA | NA |
| 101 | 6510 | 1255 | 516 | 2081 | 516 | 1112 | 6439 | 330 |
| 102 | 5652 | 4066 | 5425 | 0 | 6524 | 5737 | 7233 | 5405 |
| 103 | 8719 | 2395 | 1692 | 1131 | 3828 | 3049 | 9251 | 2018 |
| 104 | 7478 | 5097 | 6132 | 1625 | 7529 | 6630 | 9171 | 6111 |
| 105 | 2005 | 4831 | 5105 | 1631 | 3878 | 3989 | 3686 | 5866 |
| 106 | 2091 | 7553 | 6835 | 4089 | 3193 | 2842 | 5223 | 7615 |
| 107 | 2310 | 5963 | 6509 | 2498 | 4057 | 3932 | 4916 | 7270 |
| 108 | 454 | 5579 | 3469 | 2127 | 2835 | 3302 | 1876 | 4230 |
| 109 | 1115 | 4916 | 2830 | 1363 | 3701 | 4168 | 1454 | 3562 |
| 110 | 2312 | 960 | 1073 | 3894 | 4512 | 7630 | 2312 | 1258 |
| 111 | 8076 | 5300 | 3013 | 10546 | 11711 | 14194 | 8076 | 6906 |
| 112 | 2444 | 0 | 728 | 4769 | 5633 | 8562 | 2444 | 1260 |
| 113 | 4732 | 2043 | 914 | 7202 | 8368 | 10851 | 4732 | 3563 |
| 114 | 4192 | 2018 | 3033 | 165 | 2560 | 3254 | 4252 | 3034 |
| 115 | 3590 | 3198 | 4704 | 0 | 4997 | 4828 | 4743 | 4704 |
| 116 | 4704 | 1836 | 3341 | 0 | 4086 | 3466 | 5539 | 3341 |
| 117 | 3217 | 2301 | 2401 | 3900 | 3412 | 6529 | 3238 | 2539 |
| 118 | 8836 | 7570 | 6297 | 7275 | 4606 | 7657 | 8830 | 6620 |
| 119 | 9656 | 8616 | 7810 | 8788 | 6119 | 9170 | 9677 | 8133 |
| 120 | 7481 | 4206 | 5560 | 9561 | 9776 | 12856 | 7481 | 6297 |
| 121 | 7855 | 4769 | 6139 | 9722 | 8597 | 11677 | 7855 | 6651 |
| 122 | 6981 | 3706 | 5003 | 9061 | 9632 | 12712 | 6981 | 5797 |
| 123 | 11240 | 9563 | 10211 | 11248 | 8580 | 11631 | 11240 | 10396 |
| 124 | 10042 | 6768 | 7535 | 12281 | 12956 | 16036 | 10042 | 8858 |
| 125 | 6926 | 330 | 516 | 1152 | 1363 | 598 | 6958 | 495 |
| 126 | 8624 | 1828 | 537 | 1073 | 2851 | 2072 | 9049 | 1027 |
| 127 | 6559 | 1627 | 165 | 2453 | 186 | 1359 | 6488 | 171 |
| 128 | 6224 | 950 | 991 | 1606 | 1011 | 1225 | 6152 | 825 |
| 129 | 5985 | 855 | 1260 | 1259 | 1423 | 1449 | 5914 | 1237 |
| 130 | 7269 | 990 | 119 | 1791 | 676 | 275 | 7198 | 186 |
| 131 | 6956 | 495 | 351 | 1363 | 1156 | 491 | 6911 | 351 |
| 132 | 6606 | 0 | 825 | 862 | 1672 | 949 | 6696 | 825 |
| 134 | 7185 | 330 | 516 | 970 | 1575 | 676 | 7313 | 537 |
| 135 | 6783 | 0 | 1011 | 491 | 1977 | 1156 | 7054 | 1032 |
| 136 | 7986 | 1018 | 190 | 1073 | 1928 | 1150 | 8192 | 119 |
| 137 | 7651 | 760 | 537 | 676 | 2138 | 1259 | 7981 | 516 |
| 138 | 7368 | 770 | 970 | 247 | 2448 | 1568 | 7813 | 949 |
| 139 | 8624 | 1828 | 537 | 1073 | 2851 | 2072 | 9049 | 1027 |
| 140 | 8366 | 1720 | 949 | 676 | 2945 | 2166 | 8811 | 1121 |
| 141 | 8079 | 1625 | 1444 | 361 | 3159 | 2279 | 8524 | 1378 |
| 142 | 7551 | 2398 | 3062 | 808 | 4598 | 3699 | 8617 | 3010 |
| 143 | 7338 | 2185 | 2906 | 551 | 4443 | 3544 | 8361 | 2870 |
| 144 | 7148 | 2090 | 2932 | 361 | 4406 | 3507 | 8171 | 2911 |
| 145 | 7493 | 2613 | 3315 | 855 | 4851 | 3952 | 8646 | 3263 |
| 146 | 7266 | 2399 | 3159 | 599 | 4695 | 3797 | 8390 | 3138 |
| 147 | 7124 | 2257 | 3118 | 428 | 4592 | 3693 | 8219 | 3097 |
| 148 | 6270 | 1539 | 2867 | 0 | 3985 | 3179 | 7192 | 2846 |
| 149 | 5702 | 1072 | 2578 | 0 | 3510 | 2723 | 6393 | 2599 |
| 150 | 5363 | 763 | 2269 | 0 | 3013 | 2393 | 5784 | 2269 |
| 151 | 5368 | 1650 | 3155 | 0 | 4088 | 3301 | 6261 | 3176 |
| 152 | 5014 | 1402 | 2908 | 0 | 3694 | 3032 | 5719 | 2908 |
| 153 | 4717 | 1301 | 2807 | 0 | 3301 | 2931 | 5176 | 2807 |
| 154 | 4419 | 2125 | 3631 | 0 | 4291 | 3755 | 5311 | 3631 |
| 155 | 4254 | 1899 | 3405 | 0 | 3842 | 3529 | 4959 | 3405 |
| 156 | 4220 | 1798 | 3118 | 0 | 3196 | 3242 | 4540 | 3118 |
| 157 | 722 | 4110 | 1995 | 1679 | 3991 | 4458 | 637 | 2756 |
| 158 | 926 | 3990 | 1947 | 1378 | 4300 | 4767 | 855 | 2636 |
| 159 | 1586 | 3724 | 1957 | 960 | 3583 | 5736 | 1501 | 2452 |
| 160 | 309 | 3279 | 1164 | 2089 | 4664 | 5131 | 190 | 1925 |
| 161 | 832 | 2878 | 1102 | 1815 | 4101 | 5945 | 780 | 1596 |
| 162 | 1188 | 2859 | 1354 | 1824 | 3714 | 6293 | 1167 | 1663 |
| 163 | 247 | 2233 | 309 | 2585 | 4702 | 6216 | 268 | 879 |
| 164 | 970 | 2242 | 903 | 2442 | 4087 | 6596 | 991 | 1083 |
| 165 | 1342 | 2337 | 1255 | 2346 | 3754 | 6554 | 1363 | 1330 |
| 166 | 981 | 1330 | 186 | 3364 | 4917 | 7099 | 981 | 186 |
| 167 | 1177 | 1359 | 454 | 3335 | 4703 | 7249 | 1177 | 380 |
| 168 | 2290 | 1406 | 1338 | 3587 | 4066 | 7183 | 2290 | 1445 |
| 169 | 1389 | 931 | 86 | 3763 | 5058 | 7508 | 1389 | 186 |
| 170 | 2085 | 855 | 805 | 3866 | 4654 | 7772 | 2085 | 990 |
| 171 | 2435 | 1169 | 1280 | 3848 | 4304 | 7421 | 2435 | 1465 |
| 172 | 7469 | 4194 | 5394 | 9708 | 10383 | 13501 | 7469 | 6285 |
| 173 | 7479 | 4204 | 5404 | 9631 | 10231 | 13311 | 7479 | 6295 |
| 174 | 7312 | 4038 | 5237 | 9507 | 10183 | 13263 | 7312 | 6128 |
| 175 | 6410 | 3136 | 4393 | 8577 | 9252 | 12370 | 6410 | 5226 |
| 176 | 7576 | 4302 | 5694 | 9656 | 9738 | 12818 | 7576 | 6392 |
| 177 | 6910 | 3635 | 4951 | 8990 | 9547 | 12626 | 6910 | 5726 |
| 178 | 6412 | 3157 | 4625 | 8492 | 8948 | 12028 | 6412 | 5228 |
| 179 | 7459 | 4242 | 5679 | 9538 | 9444 | 12524 | 7459 | 6274 |
| 180 | 6864 | 3647 | 5100 | 8944 | 9110 | 12190 | 6864 | 5680 |
| 181 | 7837 | 4659 | 6122 | 9801 | 9302 | 12381 | 7837 | 6634 |
| 182 | 7496 | 4317 | 5780 | 9421 | 8922 | 12002 | 7496 | 6292 |
| 183 | 7273 | 4095 | 5558 | 9160 | 8684 | 11764 | 7273 | 6070 |
| 184 | 8120 | 4942 | 6405 | 9988 | 9310 | 12390 | 8120 | 6917 |
| 185 | 7928 | 4750 | 6213 | 9796 | 8901 | 11981 | 7928 | 6725 |
| 186 | 7669 | 4583 | 5953 | 9537 | 8474 | 11553 | 7669 | 6465 |
| 187 | 9656 | 8616 | 7810 | 8788 | 6119 | 9170 | 9677 | 8133 |
| 188 | 8840 | 7574 | 6301 | 7279 | 4610 | 7661 | 8834 | 6625 |
| 189 | 6556 | 5368 | 4095 | 5073 | 2404 | 5455 | 6608 | 4418 |
| 190 | 4464 | 3070 | 2066 | 2349 | 454 | 3383 | 4443 | 2346 |
| 191 | 3263 | 2969 | 3860 | 0 | 3053 | 4205 | 3301 | 3861 |
| 192 | 926 | 3348 | 1406 | 1549 | 4296 | 5367 | 832 | 2052 |
| 193 | 5407 | 5138 | 6498 | 558 | 7154 | 6810 | 7478 | 6477 |
| 194 | 2044 | 7471 | 6768 | 4022 | 3174 | 2861 | 5156 | 7548 |
| 195 | 1834 | 4873 | 4963 | 1673 | 3735 | 3885 | 3515 | 5724 |
| 196 | 723 | 4894 | 2779 | 1755 | 3350 | 3817 | 1273 | 3540 |
| 197 | 1070 | 4536 | 2450 | 1383 | 3866 | 4333 | 1150 | 3182 |
| 198 | 2861 | 5673 | 6840 | 2163 | 4608 | 4483 | 5247 | 7179 |
| 199 | 4773 | 3485 | 4949 | 0 | 5944 | 5157 | 6131 | 4949 |
| 200 | 4281 | 4019 | 2784 | 3056 | 1027 | 4144 | 4259 | 3107 |
| 201 | 5678 | 4859 | 3586 | 4522 | 1895 | 4946 | 5699 | 3909 |
| 202 | 9838 | 8161 | 8808 | 9932 | 7410 | 10461 | 9838 | 8993 |
| 203 | 8160 | 5446 | 6646 | 9330 | 7771 | 10851 | 8160 | 7018 |
| 204 | 6693 | 4042 | 5179 | 7832 | 6316 | 9396 | 6693 | 5552 |
| 205 | 3754 | 1155 | 2208 | 5621 | 6297 | 9414 | 3754 | 2581 |
| 206 | 2950 | 165 | 1234 | 5053 | 5729 | 8846 | 2950 | 1746 |
| 207 | 3891 | 703 | 2014 | 6318 | 6993 | 10010 | 3891 | 2707 |
| 208 | 5126 | 1881 | 3077 | 7495 | 8171 | 11245 | 5126 | 3942 |
| 209 | 5216 | 3635 | 2362 | 3340 | 671 | 3722 | 5195 | 2685 |
| 211 | 7071 | 4295 | 2779 | 9541 | 10707 | 13190 | 7071 | 5901 |
| 212 | 7174 | 4030 | 4123 | 9644 | 10320 | 13293 | 7174 | 6004 |
| 214 | 8259 | 5133 | 4563 | 10728 | 11480 | 14377 | 8259 | 7089 |
| 215 | 599 | 6124 | 4397 | 2839 | 2310 | 2556 | 2804 | 5177 |
| 216 | 1033 | 5664 | 4609 | 2457 | 2809 | 3017 | 3017 | 5370 |
| 217 | 1540 | 5183 | 4893 | 2029 | 3379 | 3529 | 3315 | 5654 |
| 218 | 361 | 6079 | 4041 | 2721 | 2328 | 2602 | 2448 | 4821 |
| 219 | 893 | 5365 | 4181 | 2081 | 3041 | 3315 | 2588 | 4942 |
| 220 | 1530 | 4869 | 4583 | 1673 | 3565 | 3812 | 3135 | 5344 |
| 221 | 4799 | 2066 | 1033 | 7269 | 8435 | 10917 | 4799 | 3629 |
| 222 | 4790 | 2014 | 1420 | 7260 | 8426 | 10909 | 4790 | 3621 |
| 223 | 4820 | 2043 | 1673 | 7289 | 8455 | 10938 | 4820 | 3650 |
| 224 | 5626 | 2849 | 1307 | 8095 | 9261 | 11744 | 5626 | 4456 |
| 225 | 5617 | 2841 | 1694 | 8087 | 9252 | 11735 | 5617 | 4447 |
| 226 | 5523 | 2746 | 2020 | 7992 | 9158 | 11641 | 5523 | 4353 |
| 228 | 8431 | 2832 | 2721 | 1454 | 4656 | 3777 | 9367 | 2876 |
| 229 | 6087 | 4186 | 5057 | 6688 | 5110 | 8190 | 6087 | 5242 |
| 230 | 2785 | 1640 | 1755 | 3873 | 3953 | 7070 | 2785 | 1940 |
| 231 | 7144 | 4503 | 5615 | 1198 | 6934 | 6035 | 8649 | 5594 |
| 232 | NA | NA | NA | NA | NA | NA | NA | NA |
| 233 | NA | NA | NA | NA | NA | NA | NA | NA |
| 234 | NA | NA | NA | NA | NA | NA | NA | NA |
| 235 | 11323 | 9646 | 10293 | 11331 | 8662 | 11713 | 11323 | 10478 |
| 236 | 3676 | 3177 | 4683 | 0 | 5018 | 4807 | 4828 | 4683 |
| 237 | 8365 | 5651 | 6850 | 9041 | 7222 | 10273 | 8365 | 7223 |
| 238 | 4640 | 3517 | 3694 | 5195 | 3838 | 6918 | 4640 | 3879 |
| 239 | 4625 | 2640 | 4187 | 0 | 5015 | 4228 | 5778 | 4166 |
| 240 | 5575 | 2352 | 3712 | 0 | 4811 | 4024 | 6728 | 3733 |
| 241 | 3209 | 2809 | 4191 | 0 | 4025 | 4315 | 3972 | 4191 |
The values of \(D_{ij}\) are presented on the following maps.
CityInf
InduInf
DredSit
MoorSit
RainSew
WastSew
CityWha
InduWha
vi) Weighting parameter
This corresponds to \(w_{j}\) in Formula 1.
The following table shows the weights \(w_{j}\) for each human activity:
| activity | weights |
|---|---|
| CityInf | 1 |
| InduInf | 1 |
| DredSit | 1 |
| MoorSit | 1 |
| RainSew | 1 |
| WastSew | 1 |
| CityWha | 1 |
| InduWha | 1 |
| FishTrap | 1 |
| FishTraw | 1 |
| FishLine | 1 |
| FishNet | 1 |
| FishDred | 1 |